# R script for Peak Model
#  -- generated by MACS
p <- c(0.0242137264925,0.0286162222184,0.0329371902457,0.0358721873963,0.0399485723277,0.0397039892318,0.0398670446291,0.0390517676428,0.0384810737524,0.0394594061359,0.0395409338346,0.0381549629579,0.0380734352593,0.0381549629579,0.0373396859716,0.038562601451,0.0378288521634,0.0374212136702,0.0374212136702,0.0358721873963,0.0360352427936,0.0358721873963,0.0355460766018,0.0363613535881,0.0360352427936,0.0339155226292,0.0335894118347,0.0343231611224,0.0353830212045,0.0361982981908,0.0369320474785,0.0386441291497,0.0388071845469,0.0384810737524,0.0396224615332,0.0409269047112,0.0425574586838,0.0426389863824,0.0423128755879,0.0424759309852,0.0416606539989,0.0397039892318,0.0388887122455,0.0383180183551,0.0387256568483,0.0388071845469,0.0388071845469,0.0398670446291,0.0398670446291,0.0400301000263,0.0406007939167,0.0419867647934,0.0434542633687,0.0445141234509,0.0444325957522,0.044269540355,0.0437803741632,0.0432912079715,0.0435357910673,0.0436988464646,0.0434542633687,0.0438619018618,0.0435357910673,0.0431281525742,0.0427205140811,0.0425574586838,0.0428020417797,0.0422313478893,0.0418237093961,0.0414975986016,0.0419052370948,0.0423128755879,0.0419867647934,0.0423944032865,0.0423944032865,0.0428835694783,0.0428835694783,0.0428020417797,0.0425574586838,0.0427205140811,0.0423944032865,0.0423128755879,0.0429650971769,0.0433727356701,0.0444325957522,0.0447587065468,0.0441064849577,0.0456555112317,0.0463077328207,0.0468784267111,0.0472860652042,0.047123009807,0.0472860652042,0.0467968990125,0.0463892605193,0.0457370389303,0.0465523159166,0.0451663450399,0.0452478727385,0.044921761944,0.0445956511495,0.0441064849577,0.0431281525742,0.0439434295605,0.0430466248756,0.0428020417797,0.0430466248756,0.0436988464646,0.0433727356701,0.0430466248756,0.0430466248756,0.0441064849577,0.0445956511495,0.044269540355,0.0453294004372,0.0454109281358,0.0450032896426,0.0454924558344,0.0454924558344,0.0463892605193,0.0476937036974,0.0476937036974,0.0476937036974,0.048427452985,0.0481013421905,0.0482643975878,0.0476937036974,0.0485905083823,0.0496503684644,0.0499764792589,0.0481828698891,0.0480198144919,0.048427452985,0.0487535637795,0.0480198144919,0.049079674574,0.0493242576699,0.0473675929029,0.0466338436152,0.0467968990125,0.0482643975878,0.0487535637795,0.0489981468754,0.0481013421905,0.0494057853686,0.0487535637795,0.0498134238617,0.0498949515603,0.0495688407658,0.0486720360809,0.0489981468754,0.048427452985,0.0494057853686,0.0504656454507,0.0511993947384,0.0507102285466,0.0502210623548,0.0518516163274,0.051933144026,0.0528299487109,0.0537267533958,0.0538082810945,0.0525038379164,0.0516070332315,0.0520146717246,0.0527484210123,0.0545420303821,0.0551127242725,0.0572324444368,0.0571509167382,0.0566617505464,0.0575585552313,0.0580477214231,0.0591075815053,0.0586999430121,0.0593521646012,0.0593521646012,0.0587814707108,0.0578846660259,0.0573954998341,0.0578031383272,0.0574770275327,0.0581292491217,0.058292304519,0.058292304519,0.0578846660259,0.0574770275327,0.0585368876149,0.059596747697,0.0600859138888,0.0591891092039,0.0603304969847,0.0617164678614,0.0629393833408,0.0630209110394,0.0638361880257,0.0637546603271,0.063999243423,0.0638361880257,0.0644884096147,0.065303686601,0.06595590819,0.0655482696969,0.063999243423,0.063999243423,0.0643253542175,0.0638361880257,0.0623686894504,0.0609827185737,0.0608196631765,0.061145773971,0.0597598030943,0.0595152199984,0.0604120246833,0.0609827185737,0.0613088293682,0.0623686894504,0.0638361880257,0.0655482696969,0.0666896574777,0.0658743804914,0.0657928527928,0.0655482696969,0.0648145204092,0.0655482696969,0.0649775758065,0.0649775758065,0.0651406312037,0.0652221589024,0.0643253542175,0.06595590819,0.06595590819,0.0667711851763,0.0679125729571,0.0671788236694,0.0684017391489,0.0692985438338,0.0701953485187,0.0712552086008,0.0714997916967,0.0708475701077,0.0719889578885,0.072315068683,0.0732118733679,0.0752500658336,0.075168538135,0.075820759724,0.0736195118611,0.0714997916967,0.0719074301899,0.0712552086008,0.0714182639981,0.0711736809022,0.0719889578885,0.0711736809022,0.0698692377242,0.0680756283544,0.0689724330393,0.0706029870118,0.0706845147105,0.0726411794775,0.0732118733679,0.0730488179707,0.0714997916967,0.0707660424091,0.0717443747926,0.0727227071761,0.0747608996418,0.0746793719432,0.0759022874226,0.0750054827377,0.0759022874226,0.0761468705185,0.076472981313,0.0782665906829,0.0794895061623,0.0795710338609,0.0789188122719,0.0797340892582,0.0797340892582,0.0814461709293,0.0810385324362,0.0830767249019,0.0838104741896,0.0820983925184,0.0809570047376,0.0807939493403,0.0798971446554,0.0812831155321,0.0831582526005,0.0826690864088,0.0834028356964,0.0823429756143,0.0827506141074,0.0849518619703,0.086337832847,0.0865824159429,0.0866639436415,0.0867454713402,0.0854410281621,0.0867454713402,0.086337832847,0.0851964450662,0.0855225558607,0.0837289464909,0.0860117220525,0.086990054436,0.0879683868196,0.087886859121,0.0875607483264,0.086990054436,0.0877238037237,0.0895174130935,0.0896804684908,0.09131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m <- 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ycorr <- 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altd  <- c(113)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('DOT6_rep2-GSM5884430.2x25mers.Spar+sacCer3.unique.dedup.MACS-2.1.0_model.pdf',height=6,width=6)
plot(x,p,type='l',col=c('red'),main='Peak Model',xlab='Distance to the middle',ylab='Percentage')
lines(x,m,col=c('blue'))
legend('topleft',c('forward tags','reverse tags'),lty=c(1,1,1),col=c('red','blue'))
plot(xcorr,ycorr,type='l',col=c('black'),main='Cross-Correlation',xlab='Lag between + and - tags',ylab='Correlation')
abline(v=altd,lty=2,col=c('red'))
legend('topleft','alternative lag(s)',lty=2,col='red')
legend('right','alt lag(s) : 113',bty='n')
dev.off()